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Yorodumi- PDB-7v5u: The 0.92 angstrom X-ray structure of the human heart fatty acid-b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v5u | |||||||||||||||
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Title | The 0.92 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with 2-cyclohexadecylacetic acid (CYC16AA) | |||||||||||||||
Components | Fatty acid-binding protein, heart | |||||||||||||||
Keywords | LIPID BINDING PROTEIN / FABP / complex / binding protein / 2-cyclohexadecylacetic acid | |||||||||||||||
Function / homology | Function and homology information positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å | |||||||||||||||
Authors | Sugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: To Be Published Title: The 0.92 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with 2-cyclohexadecylacetic acid (CYC16AA) Authors: Sugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v5u.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v5u.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 7v5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/7v5u ftp://data.pdbj.org/pub/pdb/validation_reports/v5/7v5u | HTTPS FTP |
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-Related structure data
Related structure data | 4wbkS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14879.022 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413 | ||||
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#2: Chemical | ChemComp-HA4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl (pH8.5), 55% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→50 Å / Num. obs: 84361 / % possible obs: 94.1 % / Redundancy: 4.9 % / Rpim(I) all: 0.02 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 0.92→0.94 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3805 / Rpim(I) all: 0.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WBK Resolution: 0.92→26.52 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.495 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.557 Å2
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Refinement step | Cycle: 1 / Resolution: 0.92→26.52 Å
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Refine LS restraints |
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